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Micholas Dean Smith, PhD
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Micholas Dean Smith PhD


Oak Ridge , Tennessee

Biography:

C.V

Education

Drexel University

Doctor of Philosophy, Physics

Dissertation Title: “Influence of aqueous-salt conditions on the structure and dynamics of the monomer and dimer forms of Alzheimer's Aβ21-30 protein fragment”

Degree Awarded in: June, 2014


Drexel University

Masters of Science, Physics

Degree Awarded in: June, 2011


Portland State University

University Honors Program: Bachelors of Science, Physics

Degree Awarded in: June, 2009


General Research Background

My research has primarily focused on the use of computational methods to study the dynamics and conformational variety of proteins and other biopolymer systems under environmental stresses, be they molecular confinement, aqueous-salt (saline) conditions, or exposure/solvation to/in organic solvents. Of particular interest is the response of naturally abundant biopolymers and/or aggregation prone proteins/peptides under these conditions for the development of novel biomaterials (and in the case of aggregation prone peptides to also gain insights into the early stages of neurodegenerative diseases).


Honors and Awards

Guoliang Yang Award for Excellence in Biophysics Research (2013), Drexel University

Best Poster (Comp. group): Unversity Research Day (2010), Drexel University


Research Experience

University of Tennessee/Oak Ridge National Laboratory

Position: Postdoctoral Research Associate Aug. 2014-Present

Center for Molecular Biophysics, Laboratory of Jeremy C. Smith

Description: Currently I am performing a series of computational investigations to elucidate the mechanisms by which water-organosolv cosolvent systems enhance the degradation of lignocellulosic biomass for the production of bio-based fuel precursors. I also initiated, and am seeking funding, for a second project focusing on the use of minimalist coarse-grained models to study mechanical properties of assemblies of randomly branched copolymers (particularly lignin, and its chemically modified variants). A third computational project focused on the use of long-time molecular dynamics sampling and information theory based metrics to enhance an ongoing drug-design project is also being pursued.


Drexel University

Graduate Research Assistant Dec. 2009-Jun. 2014

Physics Department, Laboratory of Dr. Luis Cruz Cruz

Description: I studied the interaction mechanisms between dissolved salts and the Aβ21-30 decapeptide, as well as the effects of different types of atomic-scale confinement on metastable structures of the decapeptide. Additionally, I demonstrated the existence of novel, short-lived, dimeric states of the Aβ21-30 decapeptide. In parallel, I also lead a detailed benchmarking study on how well seven common computational biophysics force-fields and water models describe the behavior of the Aβ21-30 decapeptide.


Portland State University

Undergraduate Researcher Sept. 2008-Jun. 2009

Physics Department, Laboratory of Dr. Jon Abramson

Description: Worked to develop Brownian dynamics software for the modeling of Ryanodine receptor calcium channel behavior and structure along with voltage-clamp experiments testing how electron acceptor-donor properties modify Ryanodine receptor open/closed probabilities.


Invited Talks

Drexel University, Philadelphia PA Aug, 2016

251st ACS National Meeting, Philadelphia PA Aug, 2016

University of Tennessee, Topics in Molecular Biophysics Guest Lecture Nov, 2015

249th ACS National Meeting, Denver, CO March, 2015

University of Tennessee, Topics in Molecular Biophysics Guest Lecture Nov, 2014

University of Kansas, seminar (topic) provided for the group of Wonpil Im April, 2014


Reviewer Experience

International Journal of Molecular Science

The Journal of Physical Chemistry

Frontiers in Physical Chemistry and Chemical Physics (Review Editor)

RSC Advances

IOP: Modeling and Simulation


Advising Experience


University of Tennesse/Oak Ridge National Laboratory June 2016-Present

Student. Ms. Madison K. Leonard

Project: Folding dynamics of the non-amyloid component (NAC) peptide of α-synuclein under aqueous CaCl2 and KCl salt environments


Drexel University

Student: Mr. Aquil Jones Feb. 2014-Present

Project: Influence of anionic species on the folding and dynamics of Aβ21-30


University of Tennessee/Oak Ridge National Laboratory

Student: Mr. Ian P. Kotthoff June 2015-Sept. 2015

Project: Examination of sucrose binding to the human carbonic anhydrase IX and II proteins


Drexel University

Student: Mr. Dalton Greer May 2013-Dec. 2013

Project: Computational simulations of Aβ21-30 in anionic varied salt-rich environments


Professional Affiliations

American Chemical Society: Member


Teaching Experience

Drexel University

Teaching Assistant April 2014-Jun. 2014

Supervisor: Dr. Michelle Dolinski

Course Taught: How Things Work

Description: Provide instruction to non-physics majors on the physical principles behind everyday objects. Additional responsibilities included grading of homework and providing supplementary in-class instruction.


Drexel University

Position; Teaching Assistant Jan. 2014-March 2014

Supervisor: Dr. Michel Vallieres

Course Taught: Computational Physics II

Description: Provide instruction to Physics majors on the use of C/C++ for solving ordinary differential equations and the use of random number generators. Additional responsibilities included programming solutions for students, grading of homework, providing supplementary lectures/workshops, and working closely with Dr. Vallieres in the maintenance and development of course materials.


Drexel University

Position Teaching Assistant Sept. 2013-Dec. 2013

Supervisor: Dr. Michel Vallieres

Course Taught: Advanced Computational Physics

Description: Provide instruction to Physics majors on the use of parallel computing (MPI, CUDA, Intel Xeon Phi, and Unix/TCP sockets) for solving partial differential equations. Additional responsibilities included programming solutions for students, grading of homework, providing supplementary lectures/workshops, and working closely with Dr. Vallieres in the maintenance and development of course materials.


Drexel University

Position: Teaching Assistant Sept. 2012-Dec. 2012

Supervisor: Dr. Michel Vallieres

Course Taught: Introduction to Scientific Computing

Description: Provide instruction on Linux and Maple software to undergraduate students, along with basic programming competency, while working closely with supervisor to develop student exercises. Additional responsibilities included providing one-on-one/small group assistance, lectures, grading coursework, developing supplementary course-notes, and co-designing exam exercises.


Drexel University

Position: Teaching Assistant Sept. 2009-Dec. 2009

Supervisor: Dr. Jian-Min Yuan

Course Taught: Introductory Physics (Algebra-Based)

Description: Provide instruction for two, twice a week, hour-long recitations of introductory level Physics courses and one, once a week, two-hour laboratory instruction. Responsibilities included grading coursework, proctoring examinations, and providing one-on-one help to students.


Portland State University

Position: Math and Physics Tutor Oct. 2007-Jun. 2009

Supervisor: Lisa Hatfield (Student Enhancement and Tutoring Center)

Description: Work with students of various background in small group and one-on-one tutoring sessions to review introductory level physics concepts and mathematics ranging from remedial course work to introductory differential equations.


Portland State University

Position: Physics Workshop Leader Sept. 2006-Jun. 2008

Supervisor: Dr. Ralf Widenhorn

Description: Lead small undergraduate class in problem solving methods for introductory level physics problems. Responsibilities included weekly meetings with other workshop leaders and guided instruction of students.



Outreach Experience

Philadelphia Young Chemists Committee Annual Poster Session Judge


Additional Skills:

Programming Languages:

High Level of Experience: AWK, BASH, Perl, and TCL/TK

Moderate Experience: C/C++ (including some CUDA, MPI, and OpenMP), and SED

Some Experience: Python and R

Operating Systems:

High Level of Experience: Linux (Ubuntu, Fedora, SUSE/OpenSUSE), Windows 7/8

Moderate Experience: OS X

Specialty Software:

High Level of Experience: VMD, GROMACS, xmgrace, Dynamo (Event-Driven MD software)

Moderate Experience: MAESTRO, Maple, GIMP, NWChem, and gnuplot


Publications

Effect of Ionic Aqueous Environments on the Structure and Dynamics of the of Aβ21-30 Fragment under Aqueous-Salt Solutions: An All- Atom Molecular Dynamics Study” Micholas Dean Smith & Luis Cruz, J. Phys. Chem. B DOI: 10.1021/jp312653h


Changes to the structure and dynamics in mutations of the Aβ21-30 caused by Ions in solution” Micholas Dean Smith & Luis Cruz, J. Phys. Chem. B. DOI: 10.1021/jp408579v


The Stability of a β-hairpin is altered by Surface-Water Interactions under Confinement” J. Srinivasa

Rao, Micholas Dean Smith, Luis Cruz, J. Phys. Chem. B. DOI: 10.1021/jp411122h


Spontaneous Dimer States of the Aβ21-30 Decapeptide” Micholas Dean Smith, J. Srinivasa Rao, Luis Cruz, Phys. Chem. Chem. Phys. DOI: 10.1039/C4CP01090F


Effect of Tetrahydrofuran-Water Co-Solvent on Lignin Structure and Dynamics” Micholas Dean Smith, Barmak Mostofian, Xiaolin Cheng, Loukas Petridis, Charles M. Cai, Charles E. Wyman, and Jeremy C. Smith, Green Chemistry, DOI:10.1039/C5GC01952D


Dynamics of Single Protein Molecules: Non-equilibrium and Self-Similar over Thirteen Decades in Time” Xiaohu Hu, Liang Hong, Micholas Dean Smith, Thomas Neusius, Xiaolin Cheng, and Jeremy C. Smith, Nature Physics, DOI: 10.1038/nphys3553


Force-field Induced Bias in the Structure of Aβ21-30: A Comparison of OPLS, AMBER, CHARMM and GROMOS Force-fields” Micholas Dean Smith, J. Srinivasa Rao, Luis Cruz, J. Chem. Info. Mod. DOI:10.1021/acs.jcim.5b00308


Structure and Dynamics at the onset of the Tetrahydrofuran-Water Miscibility-Gap” Micholas Dean Smith, Barmak Mostofian, Xiaolin Cheng, Loukas Petridis, and Jeremy C. Smith, J. Phys. Chem. B DOI: 10.1021/acs.jpcb.5b09770


Enhanced Sampling of Lignin Structure near the THF-Water cosolvent miscibility gap” Micholas Dean Smith, Barmak Mostofian, Xiaolin Cheng, Loukas Petridis, and Jeremy C. Smith, Phys. Chem. Chem. Phys. DOI: 10.1039/C5CP07088K


Local Phase Separation of Co-Solvents Enhanced Pretreatment of Biomass for Bioenergy Applications” Barmak Mostofian, Charles M. Cai, Micholas Dean Smith, Loukas Petridis, Xiaolin Cheng, Charles E. Wyman, and Jeremy C. Smith, J. Amer. Chem. Soc. DOI: 10.1021/jacs.6b03285


Manuscripts in Progress


Discrete Molecular Dynamics and the Behaviour of Random Hyperbranched Copolymers: An Application to the Structure of the Lignin Biopolymer”, Micholas Dean Smith, Derya Vural, and Jeremy C. Smith


Computational Screening of Cosolvent Pretreatments of Cellulosic Biomass”, Micholas Dean Smith, Barmak Mostofian, Xiaolin Cheng, Loukas Petridis, Charles M. Cai, and Jeremy C. Smith


Effect of Tetrahydrofuran-water Cosolvent on Xylose Structure and Dynamics” Micholas Dean Smith, Loukas Petridis, Xiaolin Cheng, and Jeremy C. Smith


Influence of Anionic Species on the Folding and Dynamics of Aβ21-30”, Aquil Jones, Micholas Dean Smith, Luis Cruz, In Prep


A Molecular View of the Tetrahydrofuran-Water cosolvent Enhanced Dissociation of Lignin from Cellulose in Lignocellulosic Biomass” Barmak Mostofian, Micholas Dean Smith, Xiaolin Cheng, Loukas Petridis, and Jeremy C. Smith, In Prep


Application of the Variation of Information Metric for Targeted Drug-Docking” Micholas Dean Smith, Jerome Baundry, and Jeremy C. Smith, In Prep.


Different Cations Induce Different Preferential Alignments of 21-30 dimers” Micholas Dean Smith & Luis Cruz, In Prep